Francisella tularensis subsp. tularensis group A.I, United States

Abstract

We used whole-genome analysis and subsequent characterization of geographically diverse strains using new genetic signatures to identify distinct subgroups within Francisella tularensis subsp. tularensis group A.I: A.I.3, A.I.8, and A.I.12. These subgroups exhibit complex phylogeographic patterns within North America. The widest distribution was observed for A.I.12, which suggests an adaptive advantage.

Keywords: Francisella tularensis; Francisella tularensis subsp. tularensis; SNP; United States; bacteria; geographic distribution; group A.I; phylogeography; single-nucleotide polymorphism; subgroup; tularemia.

Figure 1

Neighbor-joining tree of 14 Francisella tularensis subsp. tularensis group A.I strains constructed on the basis of single-nucleotide polymorphisms (SNPs) discovered from whole-genome sequencing. Lines represent major groups within A.I: red, A.I.12; purple, A.I.8; blue, A.I.3. Branch nomenclature for each group is indicated by green text. Bootstrap values for each group and subpopulation are indicated in black font. Pulsed-field gel electrophoresis classifications (A1a and A1b) are indicated for each sequenced strain. A.I strain SchuS4 (GenBank accession no. NC_006570) was included as a reference strain. Scale bar indicates no. SNPs.

Figure 2

Geographic alignment of 179 geographically diverse Francisella tularensis subsp. tularensis A.I strains, by subgroup, United States. A) Canonical single-nucleotide polymorphism (canSNP) topology of 15 intervening and terminal subpopulations defined by screening of 16 canSNPs. Colors indicate major subgroups within A.I: red, A.I.12; purple, A.I.8; blue, A.I.3. Subpopulations are indicated by symbols; n values indicate number of strains assigned to each subpopulation. B) Geographic distribution of strains from the 15 subpopulations, shown by corresponding symbols as in panel A and aligned by subgroup (top, A.I.12; middle, A.I.8; bottom, A.I.3). Vertical lines indicate boundaries of the 3 regions: western, central, and eastern. Subgroups are mapped on the basis of geographic origin at the state level. Gradients correspond to number of strains associated with each symbol (i.e., darker symbols indicate a higher number of strains). The basal A.I.1/3/7 subgroup (inverted triangle) cannot be meaningfully assigned to 1 of the 3 main subgroups; thus, this subgroup is arbitrarily represented on the A.I.8 map. BC, British Columbia, Canada.